Certain facts will not be in dispute at the trial, which starts today with jury selection. Johnson, 20, and his alleged victim agree they flirted at a party in February 2012, and that she was interested in him. He sent her a text message, she picked him up in her car the following night and brought him back to her house, where they began to kiss.

What happened next, however, is fiercely disputed. Johnson says they had consensual sex, but his accuser said "no" and resisted his advances, according to court documents. Afterward, she reportedly sent a text to a friend in which she wrote: "I think i might have just gotten raped …. I said no but he wouldn't listen ... ."

In a different text, however, the woman also wrote: "I don't think he did anything wrong."

A month and a half after the encounter, she filed charges against Johnson. He denies any allegations of wrongdoing.

The case has unfolded amid broad federal scrutiny of the Missoula Police Department, Missoula County District Attorney's Office and University of Montana's handling of sexual assault cases.

The U.S. Department of Justice announced in May a probe into the number of reports of sexual assaults in Missoula. During a three-year period, there were 80 reports of sexual assaults, of which 11 were at the university.

According to the DOJ, the purpose of its investigation was to determine whether the university and law enforcement agencies acted properly, adequately and fairly to protect the safety of women.

The school announced in May the NCAA had been investigating its athletic programs for undisclosed reasons.

The U.S. Department of Education, which also was looking into reports of harassment and assault allegations on campus, said Wednesday that it had closed its discrimination complaint because the allegations were being addressed by the Department of Justice investigation.

Police and university officials have been eager to cooperate with the investigations, but Missoula County Attorney Fred Van Valkenberg opposed the investigations when they were launched last year when he denied any mishandling of sexual assault reports.

The allegations have hurt the University of Montana's athletic program. In a statement to ABC News, the university said it takes its students' safety seriously and is participating and cooperating with the investigating agencies.

Read the full statement from the University of Montana below

The university also fired the Grizzlies' head coach and suspended Johnson indefinitely.

Johnson is facing up to 100 years in prison if he's convicted. Another former member of the Grizzles has also been prosecuted for rape.

Beau Donaldson, who was a running back, pleaded guilty to raping an acquaintance in September 2010. He was sentenced in January to 10 years in prison.

ABC News' Molly Maddock and The Associated Press contributed to this report.

Statement From the University of Montana
The University of Montana has been clear all along that we are participating and cooperating with the investigating agencies. UM takes the safety of our students very seriously. We work continuously – and we've been doing more in the past year – to affirm a safe campus for everyone.

This past year, we have focused on reviewing and strengthening the policies that govern how we interact with each other and our procedures for ensuring our codes of conduct are upheld; and we've worked to make sure training and education about sexual assault is in place for students and for faculty, staff and administrators.

We are proud of the tremendous work done across campus to maintain a safe learning and living environment. Recent accomplishments include implementing a campus-wide education program – an online, mandatory tutorial called PETSA (Personal Empowerment Through Self Awareness), adding another security officer on campus, and working collaboratively with the city of Missoula to address public safety concerns and other neighborhood issues.